Highly heterozygous genome phased by hifiasm, wondered added value of trio-binning?

[chhylp123]

Highly heterozygous genome phased by hifiasm, wondered added value of trio-binning?

[chhylp123]

P_ctg consists of one set of haplotype but its contigs might be switched between two haplotypes. I guess it is usually used as reference. If the paternal short reads are available, hifiasm can output fully phased assembly, i.e., two fully phased haplotypes. We think fully phased assembly should be also generated with HiC or Strand-seq if paternal data is not available, but for now hifiasm itself cannot automatically do that. If you can get phased partitioned list of HiFi reads with HiC, then feeding it to hifiasm using option '-3/-4' can also output fully phased assembly.

[zhaotao1987]

@chhylp123 Thanks very much for the reply! I see, some contigs might be switched..
btw, P_ctg is one full set of halpotype, but a_ctg is not, I think it contains only the alternative regions, I wondered how can I add the collapsed consensus regions into a_ctg as well, then I could obtain a full set of alternative haplotype (?).

[chhylp123]

It is hard. If you'd like to do it manually, probably: 1) run hifiasm with -l0, 2) find homozygous unitigs at r_utg with homozygous coverage, 3) add these unitigs to a_ctg.